DISCUSSION
Ice-cover during the last glacial maximum (LGM; 26.5-19 kya) displaced
most high-latitude species, forcing them into ice-free glacial refugia
(Hultén 1937; Hewitt 2000, 2003; Bennett & Provan 2008; Clark et
al. 2009). The largest documented LGM macro-refugium in North America
was located south of the Laurentide and Cordilleran ice sheets in the
contiguous U.S., evidenced by fossil data, climatic modeling, and
phylogeographic signatures (Graham et al. 1996; Jackson et
al. 2000; Holliday et al. 2002), although the extent and
complexity of this refugium requires further resolution. Additional LGM
refugia are hypothesized in Beringia, the area of exposed continental
shelf connecting Alaska to eastern Siberia (Hultén 1937; Abbott &
Brochmann 2003; Hope et al. 2013), and multiple smaller
micro-refugia are proposed among the archipelagos of the North Pacific
Coast (Heaton et al. 1996; Hewitt 2000; Carrara et al. 2003,
2007; Lacourse et al. 2003; Mathewes & Clague 2017), although
the duration and possible cyclic recurrence of these refugia remains
uncertain. Coastal refugia within the Alexander and Haida Gwaii
archipelagos could explain high levels of endemism in this region (Cook
& MacDonald 2001; Dawson et al. 2007) and clustered phylogenetic
breaks separating insular and continental populations (Colella et
al. 2018c; Sawyer et al. 2019) hypothesized to result from
post-glacial refugial population expansion limited by secondary contact
with closely-related, previously-allopatric taxa (Hewitt 2000).
Paleoendemic refugial persistence also explains the rapid
reestablishment of complex biotic communities so quickly following
deglaciation (Lesnek et al. 2018; Ager 2019).
Significant geographic structure within Pacific martens is consistent
with the Coastal Refugium Hypothesis (CRH) (Fig. 3, 4), suggesting the
persistence of at least one insular M. caurina population in a
North Pacific coastal refugium potentially located along the western
fringe of the Alexander or Haida Gwaii archipelagos. The two clades
within M. caurina are genetically distinct, parsing an insular
and continental lineage, despite mitochondrial nesting (Fig. 2d;
Supplemental Information 5). The two insular and continental M.
caurina clades are geographically discontinuous (Fig. 1) and estimated
to have diverged almost 1 million years ago (Fig. 3b), although PSMC
date estimates are highly sensitive to scaling (mutation rate and
generation time). Divergence predating the most recent interglacial
suggests that insular M. caurina may have diverged from
continental populations over multiple glacial cycles, perhaps initially
in a coastal refugium and then subsequently on one or more NPC islands.
Our genomic results initially contradict the fossil record, which shows
a scarcity of fossils on POW Island during the LGM
(~20-15 kya, Lesnek et al. 2018) and documents
martens appearing on POW during the late Pleistocene (>14
kya) and early Holocene (9-14 kya, Heaton & Grady 2003; Pauli et al.
2015). Absence of martens and other mammals in the Southeast Alaskan
fossil record during the LGM may reflect sampling bias, as most dated
fossil materials from the region were collected from the Shuká Káa cave
at the northern end of POW. Insular M. caurina have not been
documented on POW and this site was likely ice-covered at the peak of
the LGM (Lesnek et al. 2018). Even so, a number of meso-carnivore
teeth from Shuká Káa cave morphologically identified as mink
(Mustela vison ) may instead mark the early presence of insularM. caurina (Heaton & Grady 2003), as these species have similar
tooth morphology. Similar to misidentifications of Pleistocene coastal
black bear (Ursus americanus ) fossils from POW that were
originally listed as brown bears (Ursus arctos ) due to size
differences over evolutionary timescales (Lindqvist pers.
obs.), insular M. caurina are physically larger than bothM. americana and continental M. caurina (Colella et al.
2018b) which may confound taxonomic assignment of dentition. The
persistence of diverse communities of large terrestrial mammals,
including caribou, bears, and foxes, evident in the fossil record both
pre- and post-LGM (Lesnek et al. 2018), points to a higher
potential for local refugial persistence through the LGM over the
recolonization of these outer islands from mainland sources since the
Holocene (Ager 2019).
The viability of a coastal migration route for human colonization of the
Americas hinges on our understanding of glacial extent and biotic
community composition along the NPC during the late Pleistocene.
Geological investigations of southeast Alaska have produced mixed
results. Bathymetry (Carrara et al. 2003, 2007) and palynology (Ager
2019) support the persistence of coastal refugia, while cosmogenic
exposure dating has shed doubt on hypothesized refugial locations
(Lesnek et al. 2018). Multiple signatures of refugial persistence across
taxa (Foster 1965; Heaton et al. 1996; Hewitt 2000, 2003; Weckworth et
al. 2005; Colella et al. 2018c; Sawyer et al. 2019) is
detailing increasingly complex refugial communities along the coast.
For marten, the laterally dilated cranial shape of insular M.
caurina hints at a dietary shift towards the consumption of marine prey
items (Colella et al. 2018b), also documented in stomach contents
(Giannico & Nagorsen 1989) and also reflected in insular wolves of the
NPC (Darimont et al. 2009; Muñoz-Fuentes et al. 2010).
Martens rely on deep persistent snow and complex forest structure
(Proulx 1997; Pauli et al. 2013; Manlick et al. 2017; Martin et al.
2019) for predator avoidance, thermal management, and efficient
locomotion, suggesting that refugial ecosystems would have contained
forest community assemblages. Access to both marine and terrestrial prey
items and timber resources along a NPC migration route, would have
enhanced human survivorship during an early pulse of human migration
into the Americas via the Pacific coast (Fladmark 1979; Dixon 1993).
The insular-continental biogeographic and phylogenetic break withinM. caurina is largely consistent with signatures from numerous
other NPC paleoendemics (bears, Heaton et al. 1996; deer, Latchet al. 2009; ermine, Colella et al. 2018c; shrews,
Demboski & Cook 2001; deer mice, Sawyer et al. 2019) and also
evident in the few associated parasites examined to date
(Soboliphyme baturini , Koehler et al. 2007, 2009; Hoberget al. 2012). Disparate distributions of insular lineages across
these heterogeneous archipelagos suggests that the geographic pattern
and duration of refugial isolation may vary across climate cycles,
depending on the ecological plasticity and dispersal abilities of
incumbent species. Insular ‘ABC’ brown bears (Ursus arctos,Heaton et al. 1996), for example, are currently geographically
restricted to the three northern most islands of the Alexander
Archipelago (Admiralty, Baranof, Chichagof), while the insular black
bear lineage (Byun et al. 1997) has a more southerly distribution
encompassing southern Alexander Archipelago islands, the Haida Gwaii
Archipelago, Vancouver Island, and coastal British Columbia. Under the
assumption of niche conservatism, this phylogeographic pattern suggests
a cooler, northern refugium within the Alexander Archipelago and a
slightly warmer, perhaps more heavily vegetated refugial ecosystem to
the south, either in the southern Alexander Archipelago or Haida Gwaii.
Early paleoclimatic models for NPC refugia hypothesized these areas to
be primarily tundra and unable to support forest-associated taxa such as
black bears and martens (Hansen & Engstrom 1996; Ager 2007). More
recently however, palynological investigations and radiocarbon dating of
postglacial peat and sediment cores indicate that coastal forests
similar to today’s forests existed in the Alexander Archipelago during
the last interglacial (Ager 2019). Rapid colonization of the
western-most islands by pine trees (Picea ) immediately following
glacial recession (~17 kya) hints at the potential
refugial persistence of coniferous forests (Lesnek et al. 2018; Ager
2019) and parallels our hypothesis that refugial persistence of insularM. caurina is more likely than post-glacial recolonization.
Comparative demography also identified at least three major evolutionary
trajectories: M. americana, continental M. caurina (Fig.
3b) and insular M. caurina, consistent with the CRH. Martes
americana distributions of effective population size are overall higher
than those of M. caurina clades, consistent with the contiguous
contemporary range of this species and historical divergence in and
subsequent expansion from a single, large eastern refugium (Stoneet al. 2002). Within M. americana , Chichagof Island
exhibits the highest effective population size (Ne),
followed by central Alaska (Fig. 3b). Although high Neis surprising for an insular population, Chichagof Island received
iterative translocations of M. americana in the mid-1900s from
multiple source populations, including four other islands in southeast
Alaska (Baranof, Wrangell, Mitkof [Petersburg], and Revillagigedo
[Ketchikan] islands) and one distant continental locality (Polly
Creek, in central AK). These introductions may inflate population size
estimates as a consequence of outbreeding (Paul 2009) and make the
historical distribution of Ne for this individual
resemble that of its source populations (e.g., MAK). In contrast, Prince
of Wales Island (POW) received introductions from only two proximate
sources: Revillagigedo and Mitkof islands (Burris & McKnight 1973).
Revillagigedo Island shows a similar demographic history to POW,
suggesting those translocations resulted in successful establishment
(Elkins & Nelson 1954). Although our results hint at
insular-continental structure within M. americana (Fig. 3), this
signal is muddled by historical wildlife translocations and remains
unresolved from a nuclear perspective (Fig. 2). Relative to M.
americana , both continental and insular M. caurina have
persistently smaller effective population sizes.
Among continental species, a common response to rising temperatures is
the upward distributional shift in elevation (or latitude) to retain
suitable environmental conditions (Hampe & Jump 2011). The fragmented
contemporary distribution of continental M. caurina populations
(U.S. west coast, Pacific Northwest forests, mountaintops of the
American Southwest; Fig. 1) is consistent with the retention of a cooler
paleoclimatic niche for species experiencing increasing fragmentation
under current warming conditions (Brown 1971; Anderson et al.2000; Parmesan 2006; Hampe & Jump 2011; Meng et al. 2019).
Relative to all continental taxa, insular M. caurina show a
significantly depressed effective population size through time, with the
highest overall inbreeding coefficients. Although likely a consequence
of island life, small effective population sizes and high levels of
inbreeding place insular martens at an elevated risk of extinction
(Frankham 1998; Rybicki & Hanski 2013).
Refugial divergence along the NPC also explains the disjunct
contemporary distribution of M. caurina (Fig. 1). Along the NPC,M. caurina inhabits at least three islands; however, Admiralty
Island in Southeast Alaska is more than 300 km north of the two insular
Canadian populations. Although geographic disjunction across three
islands is substantial, the genetic similarly of these island
populations points to historical divergence in a single coastal refugium
and a potentially more widespread historical distribution of insularM. caurina throughout NPC islands. Higher density sampling across
the NPC will be necessary to refine the geographic limits of insular and
continental M. caurina clades. Refugial divergence of insularM. caurina is further supported by the persistence of the insular
lineage in the Kuiu Island hybrid zone (Dawson et al. 2017),
~20km south of Admiralty Island, relictual signatures ofM. caurina on POW (Pauli et al. 2015), and associated
nematodes (Soboliphyme baturini ) on Chichagof Island (Koehleret al. 2007, 2009; Hoberg et al. 2012). Chichagof martens
harbor distinctive nematodes that are phylogenetically close to S.
baturini found in other populations of M. caurina , suggestingM. caurina or a ‘ghost’ marten lineage may persist or have
persisted on this island until relatively recently (Koehler et
al. 2007, 2009; Hoberg et al. 2012). Similarly, POW is
hypothesized to have been colonized by multiple natural sources (Pauliet al. 2015) and iterative translocations of M. americanato this island were surprisingly successful considering as few as 10
martens (4 females) were introduced to the island (Paul 2009). In
contrast, our genomic analyses did not find M. caurina alleles in
either of the individuals sequenced from islands that received
translocations of M. americana . Instead, we found each island to
be genetically aligned with M. americana and their translocation
source populations: Chichagof Island with central Alaska and POW with
Revillagigedo Island (Fig. 2 and 3). Overall our results suggest thatM. caurina were either not present on these islands prior to
translocations or were recently replaced or swamped by introduced or
invading M. americana . Interspecific competition, outbreeding, or
the introduction of foreign pathogens among other variables may have
impacted native M. caurina (Plein et al. 2016; Colellaet al. 2018b; Northover et al. 2018). Ultimately, until
additional hybrids are sequenced, our results discourage the
translocation of American marten for the genetic rescue or restoration
of coastal martens due to potential swamping and emphasize the
importance of careful source population selection, as the NPC harbors
significant cryptic diversity and complex evolutionary histories.
We detected a hybrid individual collected from each natural mixing zone:
Kuiu Island Alaska and western Montana in the northern Rocky Mountains
(Table 2; Fig. 2-4; Supplemental Information 9-16). Both hybrids were
female, had M. americana mitochondrial haplotypes (Fig. 2d), and
mixed nuclear ancestry, with the Montana hybrid containing continentalM. caurina alleles and the Kuiu hybrid containing insularM. caurina alleles (Table 2; Supplemental Information 10-13,
16-17). Both admixed individuals were identified as early
generational-stage hybrids (e.g., F1’s or a single generation
backcrossed with M. americana , Supplemental Information 11-12)
with introgression occurring recently (Supplemental Information 21).
Although sample sizes are small, the absence of late-generational
hybrids is surprising, especially for the Montana zone which has
persisted for many generations (Wright 1953). Detection of only
early-generational hybrids is consistent with the presence of hybrid
incompatibilities, where F1 hybrids experience a temporary elevation in
fitness (heterosis) compared to later generational-stage hybrids (e.g.,
F2 and beyond) that may suffer outbreeding depression as a result of
disrupted co-adapted gene complexes (Todesco et al. 2016). The
disruption of co-adapted gene complexes or genes involved in local
adaptation via introgression, and particularly loci involved in disease
and pathogen resistance (Alibert et al. 1994), may pose a
particular challenge to naïve insular taxa. This hypothesis warrants
further genomic investigation with fine-scale sampling from within
hybrid zones and translocated islands.
Differentiation between insular and continental M. caurina was
suggested previously based on reduced-representation genetic approaches
(Demboski et al. 1999, 2001; Stone et al. 2002; Smallet al. 2003; Dawson et al. 2017), but the extent of
divergence was unknown. A genomic pattern of refugial divergence may be
more widespread than previously suspected and additional
forest-associated taxa, that are not well represented in the fossil
record, may have persisted in NPC refugia. Our results underscore the
importance of reevaluating work previously based on one or a few genes,
as genomic resolution continues to provide unexpected insight into the
evolutionary complexities of coastal refugia (Miller et al. 2012;
Colella et al. 2018c) and complex landscapes and holds great promise to
unravel complexity across time.